Summarise the taxonmic distribution across different sample types in the Earth Microbiome Project

The Earth Microbiome Project (EMP) is collaborative effort to curate and characterise microbial taxonomy and function on Earth (Thompson et al. 2017).
The aim of this script is to summarise the taxonmic distribution across different sample types, as defined by the EMP. The script summarises phyla by default but can also summarise the sequences at different taxonimc levels. The script uses the 3rd calssification level of the EMP Ontology (empo_3), but this can also be altered.

Set main parameters and download data tables from the EMP FTP site

ftp <- "ftp://ftp.microbio.me/emp/release1/"
biom_file <- "emp_cr_silva_16S_123.subset_10k.biom"
map_file <- "emp_qiime_mapping_subset_10k.tsv"
new_map_file <- "emp_qiime_mapping_subset_10k_noBLNK.csv"
Rank <- "Phylum"
Grouping_var <- "empo_3"
EMPO_levels2keep <- c("Soil (non-saline)", "Plant rhizosphere", "Animal corpus", "Water (saline)", "Sediment (saline)", "Water (non-saline)", "Hypersaline (saline)", "Sediment (non-saline)", "Animal distal gut", "Animal proximal gut", "Aerosol (non-saline)", "Animal secretion", "Animal surface", "Plant corpus", "Surface (non-saline)", "Plant surface", "Surface (saline)") # remove unwanted environments
biom_ftp <- paste0(ftp, "otu_tables/closed_ref_silva/", biom_file)
map_ftp <- paste0(ftp, "mapping_files/", map_file)
download.file(biom_ftp, biom_file)
download.file(map_ftp, map_file)

# fill-in missing values with NA, convert to CSV
system("awk 'BEGIN { FS = OFS = \"\t\" } { for(i=1; i<=NF; i++) if($i ~ /^ *$/) $i = \"NA\" }; 1' emp_qiime_mapping_subset_2k.tsv  |  awk 'BEGIN { FS=\",\"; OFS=\";\" } {$1=$1; print}' |  awk 'BEGIN { FS=\"\t\"; OFS=\",\" } {$1=$1; print}' > emp_qiime_mapping_subset_10k_noBLNK.csv")

Generate a phyloseq object from the biom and (modified) map files

(EMP_otu_tax <- import_biom(biom_file, parseFunction = parse_taxonomy_silva_128, 
                            parallel = TRUE))
## phyloseq-class experiment-level object
## otu_table()   OTU Table:          [ 126730 taxa and 10000 samples ]:
## tax_table()   Taxonomy Table:     [ 126730 taxa by 7 taxonomic ranks ]:
## taxa are rows
read_csv(new_map_file,
                    trim_ws = TRUE) %>% 
  column_to_rownames("#SampleID") %>% 
  sample_data() ->
  EMP_map

EMP <- merge_phyloseq(EMP_otu_tax, EMP_map)

# for debugging and testing
# EMP %>%
#   subset_samples(empo_3 %in% EMPO_levels2keep) %>%
#   prune_samples(sample_names(.)[sample(1:nsamples(.), 100)], .) %>%
#   phyloseq::filter_taxa(., function(x) sum(x) > 0, TRUE) %>%
#   prune_taxa(taxa_names(.)[sample(1:ntaxa(.), 1000)], .) ->
#   EMP_subset

EMP %>% 
  PS_merge_samples(grouping_name = Grouping_var, fun = "mean") ->
  EMP_merge

Generate a summary table of taxonomic distributions across sample types

# summarise abundance by environment and phylum
EMP_merge %>%
  tax_glom(taxrank = Rank) %>%                     # agglomerate at 'Rank' level
  psmelt() %>%                                         # Melt to long format
  arrange(Rank)  %>%                                  # arrange by 'Rank'
  group_by_at(c(Grouping_var, Rank)) %>% 
  # summarise and create a column with the relative abundance
  summarise(Abundance = sum(Abundance)) %>%
  mutate(Rreq = paste0(round(100 * Abundance / sum(Abundance), 2), "%")) ->
  taxa_sum_df

# determine the phylum order by decreasing abundance (for plotting)
EMP_merge %>%
  tax_glom(taxrank = Rank) %>%                     # agglomerate at 'Rank' level
    transform_sample_counts(., function(x) x / sum(x) ) %>% 
  psmelt() %>%                                        # Melt to long format
  arrange(Rank)  %>%                                  # arrange by 'Rank'
  group_by_at(c("OTU", Rank)) %>% 
  summarise(Abundance = sum(Abundance)) %>%
  arrange(Abundance) ->
  Rank_order 

# print summary table
taxa_sum_df %>% 
  filter(Abundance != 0) %>%
  kable(., digits = c( 0, 1)) %>%
  kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = F)
empo_3 Phylum Abundance Rreq
Aerosol (non-saline) Acidobacteria 65715 0.8%
Aerosol (non-saline) Actinobacteria 718035 8.73%
Aerosol (non-saline) Aerophobetes 3 0%
Aerosol (non-saline) Aminicenantes 114 0%
Aerosol (non-saline) aquifer1 2131 0.03%
Aerosol (non-saline) Armatimonadetes 7036 0.09%
Aerosol (non-saline) Atribacteria 171 0%
Aerosol (non-saline) Bacteroidetes 825065 10.03%
Aerosol (non-saline) Caldiserica 3 0%
Aerosol (non-saline) Candidate division OP3 149 0%
Aerosol (non-saline) Candidate division SR1 3317 0.04%
Aerosol (non-saline) Chlamydiae 571 0.01%
Aerosol (non-saline) Chlorobi 645 0.01%
Aerosol (non-saline) Chloroflexi 22528 0.27%
Aerosol (non-saline) Cloacimonetes 349 0%
Aerosol (non-saline) Cyanobacteria 1425687 17.33%
Aerosol (non-saline) Deferribacteres 12 0%
Aerosol (non-saline) Deinococcus-Thermus 2993 0.04%
Aerosol (non-saline) Elusimicrobia 759 0.01%
Aerosol (non-saline) Euryarchaeota 6509 0.08%
Aerosol (non-saline) Fibrobacteres 2681 0.03%
Aerosol (non-saline) Firmicutes 2384579 28.98%
Aerosol (non-saline) Fusobacteria 71051 0.86%
Aerosol (non-saline) GAL08 1 0%
Aerosol (non-saline) Gemmatimonadetes 17409 0.21%
Aerosol (non-saline) Gracilibacteria 13 0%
Aerosol (non-saline) Hyd24-12 11 0%
Aerosol (non-saline) Hydrogenedentes 195 0%
Aerosol (non-saline) JL-ETNP-Z39 28 0%
Aerosol (non-saline) Latescibacteria 189 0%
Aerosol (non-saline) Lentisphaerae 2958 0.04%
Aerosol (non-saline) Marinimicrobia (SAR406 clade) 498 0.01%
Aerosol (non-saline) Microgenomates 3 0%
Aerosol (non-saline) Miscellaneous Crenarchaeotic Group 15 0%
Aerosol (non-saline) Nitrospirae 2424 0.03%
Aerosol (non-saline) Omnitrophica 3 0%
Aerosol (non-saline) Parcubacteria 660 0.01%
Aerosol (non-saline) PAUC34f 2 0%
Aerosol (non-saline) Planctomycetes 17895 0.22%
Aerosol (non-saline) Proteobacteria 2538308 30.85%
Aerosol (non-saline) Saccharibacteria 2235 0.03%
Aerosol (non-saline) SHA-109 335 0%
Aerosol (non-saline) SM2F11 5 0%
Aerosol (non-saline) Spirochaetae 14928 0.18%
Aerosol (non-saline) Synergistetes 1844 0.02%
Aerosol (non-saline) TA06 9 0%
Aerosol (non-saline) Tenericutes 14461 0.18%
Aerosol (non-saline) Thaumarchaeota 6196 0.08%
Aerosol (non-saline) Thermotogae 5877 0.07%
Aerosol (non-saline) TM6 970 0.01%
Aerosol (non-saline) uncultured archaeon 1 0%
Aerosol (non-saline) Verrucomicrobia 59161 0.72%
Aerosol (non-saline) WCHB1-60 9 0%
Aerosol (non-saline) WD272 1656 0.02%
Aerosol (non-saline) Woesearchaeota (DHVEG-6) 2 0%
Animal corpus Acetothermia 47 0%
Animal corpus Acidobacteria 33383 0.65%
Animal corpus Actinobacteria 940836 18.35%
Animal corpus Aerophobetes 243 0%
Animal corpus Aminicenantes 244 0%
Animal corpus aquifer1 23 0%
Animal corpus Aquificae 12 0%
Animal corpus Armatimonadetes 2576 0.05%
Animal corpus Atribacteria 1014 0.02%
Animal corpus Bacteroidetes 265073 5.17%
Animal corpus Caldiserica 2 0%
Animal corpus Candidate division OP3 118 0%
Animal corpus Candidate division SR1 58 0%
Animal corpus Chlamydiae 114 0%
Animal corpus Chlorobi 926 0.02%
Animal corpus Chloroflexi 2474 0.05%
Animal corpus Cyanobacteria 123478 2.41%
Animal corpus Deferribacteres 52 0%
Animal corpus Deinococcus-Thermus 474 0.01%
Animal corpus Elusimicrobia 17 0%
Animal corpus Euryarchaeota 416 0.01%
Animal corpus Fibrobacteres 58 0%
Animal corpus Firmicutes 540593 10.54%
Animal corpus Fusobacteria 9791 0.19%
Animal corpus Gemmatimonadetes 2488 0.05%
Animal corpus GOUTA4 10 0%
Animal corpus Gracilibacteria 7 0%
Animal corpus Hyd24-12 54 0%
Animal corpus Hydrogenedentes 40 0%
Animal corpus JL-ETNP-Z39 20 0%
Animal corpus Latescibacteria 12 0%
Animal corpus LCP-89 8 0%
Animal corpus Lentisphaerae 29 0%
Animal corpus Marinimicrobia (SAR406 clade) 920 0.02%
Animal corpus Microgenomates 3 0%
Animal corpus Miscellaneous Crenarchaeotic Group 4 0%
Animal corpus Nitrospirae 268 0.01%
Animal corpus Parcubacteria 35 0%
Animal corpus Planctomycetes 1799 0.04%
Animal corpus Proteobacteria 3180203 62.02%
Animal corpus Saccharibacteria 181 0%
Animal corpus SHA-109 12 0%
Animal corpus SM2F11 12 0%
Animal corpus Spirochaetae 544 0.01%
Animal corpus Synergistetes 163 0%
Animal corpus TA06 6 0%
Animal corpus Tenericutes 7571 0.15%
Animal corpus Thaumarchaeota 584 0.01%
Animal corpus Thermotogae 39 0%
Animal corpus TM6 137 0%
Animal corpus Verrucomicrobia 10794 0.21%
Animal corpus WCHB1-60 16 0%
Animal corpus WD272 2 0%
Animal corpus Woesearchaeota (DHVEG-6) 1 0%
Animal distal gut Acidobacteria 1368 0.02%
Animal distal gut Actinobacteria 255935 2.81%
Animal distal gut Aerophobetes 1 0%
Animal distal gut Aminicenantes 6 0%
Animal distal gut aquifer1 17 0%
Animal distal gut Armatimonadetes 306 0%
Animal distal gut Bacteroidetes 1915725 21.05%
Animal distal gut Caldiserica 6 0%
Animal distal gut Candidate division OP3 2 0%
Animal distal gut Candidate division SR1 8 0%
Animal distal gut Chlamydiae 78 0%
Animal distal gut Chlorobi 33 0%
Animal distal gut Chloroflexi 2520 0.03%
Animal distal gut CKC4 1039 0.01%
Animal distal gut Cyanobacteria 173918 1.91%
Animal distal gut Deferribacteres 42 0%
Animal distal gut Deinococcus-Thermus 306 0%
Animal distal gut Elusimicrobia 1639 0.02%
Animal distal gut Euryarchaeota 29710 0.33%
Animal distal gut Fibrobacteres 3715 0.04%
Animal distal gut Firmicutes 3899629 42.84%
Animal distal gut Fusobacteria 127764 1.4%
Animal distal gut Gemmatimonadetes 117 0%
Animal distal gut Gracilibacteria 252 0%
Animal distal gut Hydrogenedentes 13 0%
Animal distal gut Kazan-3B-09 1 0%
Animal distal gut Latescibacteria 19 0%
Animal distal gut Lentisphaerae 15139 0.17%
Animal distal gut Marinimicrobia (SAR406 clade) 98 0%
Animal distal gut Microgenomates 9 0%
Animal distal gut Miscellaneous Crenarchaeotic Group 1 0%
Animal distal gut Nitrospirae 82 0%
Animal distal gut Omnitrophica 1 0%
Animal distal gut Parcubacteria 9 0%
Animal distal gut Planctomycetes 17076 0.19%
Animal distal gut Proteobacteria 2414998 26.53%
Animal distal gut RsaHF231 41 0%
Animal distal gut Saccharibacteria 391 0%
Animal distal gut SHA-109 273 0%
Animal distal gut Spirochaetae 45267 0.5%
Animal distal gut Synergistetes 1914 0.02%
Animal distal gut TA06 2 0%
Animal distal gut Tenericutes 93010 1.02%
Animal distal gut Thaumarchaeota 107 0%
Animal distal gut TM6 49 0%
Animal distal gut Verrucomicrobia 99716 1.1%
Animal distal gut WCHB1-60 27 0%
Animal distal gut WD272 4 0%
Animal distal gut Woesearchaeota (DHVEG-6) 2 0%
Animal proximal gut Acidobacteria 2004 0.03%
Animal proximal gut Actinobacteria 522437 6.87%
Animal proximal gut aquifer1 43 0%
Animal proximal gut Aquificae 5 0%
Animal proximal gut Armatimonadetes 91 0%
Animal proximal gut Bacteroidetes 1588077 20.87%
Animal proximal gut Caldiserica 4 0%
Animal proximal gut Candidate division OP3 1 0%
Animal proximal gut Candidate division SR1 282 0%
Animal proximal gut Chlamydiae 78 0%
Animal proximal gut Chlorobi 38 0%
Animal proximal gut Chloroflexi 1631 0.02%
Animal proximal gut Cyanobacteria 198842 2.61%
Animal proximal gut Deferribacteres 112 0%
Animal proximal gut Deinococcus-Thermus 548 0.01%
Animal proximal gut Elusimicrobia 52 0%
Animal proximal gut Euryarchaeota 15879 0.21%
Animal proximal gut Fibrobacteres 14306 0.19%
Animal proximal gut Firmicutes 3358560 44.14%
Animal proximal gut Fusobacteria 11470 0.15%
Animal proximal gut Gemmatimonadetes 601 0.01%
Animal proximal gut Gracilibacteria 32 0%
Animal proximal gut Hydrogenedentes 3 0%
Animal proximal gut Latescibacteria 3 0%
Animal proximal gut Lentisphaerae 9934 0.13%
Animal proximal gut Marinimicrobia (SAR406 clade) 2 0%
Animal proximal gut Nitrospirae 39 0%
Animal proximal gut Omnitrophica 8 0%
Animal proximal gut Parcubacteria 5 0%
Animal proximal gut PAUC34f 1 0%
Animal proximal gut Planctomycetes 89883 1.18%
Animal proximal gut Proteobacteria 1371070 18.02%
Animal proximal gut Saccharibacteria 57 0%
Animal proximal gut SHA-109 337 0%
Animal proximal gut SM2F11 1 0%
Animal proximal gut Spirochaetae 137338 1.8%
Animal proximal gut Synergistetes 2241 0.03%
Animal proximal gut Tenericutes 21776 0.29%
Animal proximal gut Thaumarchaeota 568 0.01%
Animal proximal gut Thermotogae 4 0%
Animal proximal gut TM6 56 0%
Animal proximal gut Verrucomicrobia 261203 3.43%
Animal proximal gut WCHB1-60 5 0%
Animal proximal gut WD272 80 0%
Animal proximal gut Woesearchaeota (DHVEG-6) 35 0%
Animal secretion Acidobacteria 7412 0.1%
Animal secretion Actinobacteria 750903 10.03%
Animal secretion Aerophobetes 1 0%
Animal secretion Aminicenantes 32 0%
Animal secretion aquifer1 7206 0.1%
Animal secretion Armatimonadetes 604 0.01%
Animal secretion Bacteroidetes 982127 13.12%
Animal secretion Candidate division OP3 2 0%
Animal secretion Candidate division SR1 4813 0.06%
Animal secretion Chlamydiae 781 0.01%
Animal secretion Chlorobi 683 0.01%
Animal secretion Chloroflexi 5634 0.08%
Animal secretion Crenarchaeota 1 0%
Animal secretion Cyanobacteria 46048 0.62%
Animal secretion Deferribacteres 48 0%
Animal secretion Deinococcus-Thermus 5777 0.08%
Animal secretion Elusimicrobia 36 0%
Animal secretion Euryarchaeota 842 0.01%
Animal secretion Fibrobacteres 21 0%
Animal secretion Firmicutes 2390653 31.94%
Animal secretion Fusobacteria 309677 4.14%
Animal secretion Gemmatimonadetes 3799 0.05%
Animal secretion GOUTA4 2 0%
Animal secretion Gracilibacteria 917 0.01%
Animal secretion Hydrogenedentes 241 0%
Animal secretion JL-ETNP-Z39 17 0%
Animal secretion Latescibacteria 56 0%
Animal secretion LCP-89 1 0%
Animal secretion Lentisphaerae 162 0%
Animal secretion Marinimicrobia (SAR406 clade) 471 0.01%
Animal secretion Microgenomates 49 0%
Animal secretion Miscellaneous Crenarchaeotic Group 17 0%
Animal secretion Nitrospirae 786 0.01%
Animal secretion OC31 1 0%
Animal secretion Omnitrophica 1 0%
Animal secretion Parcubacteria 160 0%
Animal secretion PAUC34f 2 0%
Animal secretion Planctomycetes 3125 0.04%
Animal secretion Proteobacteria 2792267 37.3%
Animal secretion Saccharibacteria 6599 0.09%
Animal secretion SHA-109 31 0%
Animal secretion SM2F11 15 0%
Animal secretion Spirochaetae 7108 0.09%
Animal secretion Synergistetes 967 0.01%
Animal secretion TA06 17 0%
Animal secretion Tenericutes 148187 1.98%
Animal secretion Thaumarchaeota 627 0.01%
Animal secretion TM6 61 0%
Animal secretion Verrucomicrobia 6691 0.09%
Animal secretion WCHB1-60 29 0%
Animal secretion WD272 25 0%
Animal secretion Woesearchaeota (DHVEG-6) 18 0%
Animal surface Acidobacteria 22815 0.24%
Animal surface Actinobacteria 1195171 12.54%
Animal surface Aerophobetes 2 0%
Animal surface Aminicenantes 13 0%
Animal surface aquifer1 797 0.01%
Animal surface Armatimonadetes 4434 0.05%
Animal surface Atribacteria 29 0%
Animal surface Bacteroidetes 939832 9.86%
Animal surface Caldiserica 4 0%
Animal surface Candidate division OP3 13 0%
Animal surface Candidate division SR1 796 0.01%
Animal surface Chlamydiae 334 0%
Animal surface Chlorobi 908 0.01%
Animal surface Chloroflexi 10418 0.11%
Animal surface CKC4 26 0%
Animal surface Cloacimonetes 4 0%
Animal surface Cyanobacteria 208679 2.19%
Animal surface Deferribacteres 72 0%
Animal surface Deinococcus-Thermus 8109 0.09%
Animal surface Elusimicrobia 157 0%
Animal surface Euryarchaeota 937 0.01%
Animal surface Fibrobacteres 157 0%
Animal surface Firmicutes 1931918 20.27%
Animal surface Fusobacteria 107148 1.12%
Animal surface GAL08 1 0%
Animal surface Gemmatimonadetes 8330 0.09%
Animal surface GOUTA4 1 0%
Animal surface Gracilibacteria 360 0%
Animal surface Hydrogenedentes 500 0.01%
Animal surface JL-ETNP-Z39 17 0%
Animal surface Latescibacteria 170 0%
Animal surface LCP-89 1 0%
Animal surface Lentisphaerae 946 0.01%
Animal surface Marine Hydrothermal Vent Group(MHVG) 5 0%
Animal surface Marinimicrobia (SAR406 clade) 42 0%
Animal surface Microgenomates 11 0%
Animal surface Miscellaneous Crenarchaeotic Group 17 0%
Animal surface Nitrospirae 1271 0.01%
Animal surface OC31 1 0%
Animal surface Omnitrophica 48 0%
Animal surface Parcubacteria 45 0%
Animal surface PAUC34f 186 0%
Animal surface Planctomycetes 11390 0.12%
Animal surface Proteobacteria 4884024 51.25%
Animal surface RsaHF231 11 0%
Animal surface Saccharibacteria 433 0%
Animal surface SHA-109 688 0.01%
Animal surface SM2F11 8 0%
Animal surface Spirochaetae 2301 0.02%
Animal surface Synergistetes 351 0%
Animal surface TA06 188 0%
Animal surface Tenericutes 153480 1.61%
Animal surface Thaumarchaeota 1351 0.01%
Animal surface Thermotogae 17 0%
Animal surface TM6 239 0%
Animal surface uncultured archaeon 1 0%
Animal surface Verrucomicrobia 30320 0.32%
Animal surface WCHB1-60 158 0%
Animal surface WD272 161 0%
Animal surface Woesearchaeota (DHVEG-6) 17 0%
Hypersaline (saline) Acetothermia 3106 0.34%
Hypersaline (saline) Acidobacteria 19360 2.09%
Hypersaline (saline) Actinobacteria 47574 5.15%
Hypersaline (saline) Aenigmarchaeota 210 0.02%
Hypersaline (saline) Aerophobetes 77 0.01%
Hypersaline (saline) Aminicenantes 1274 0.14%
Hypersaline (saline) Armatimonadetes 1078 0.12%
Hypersaline (saline) Atribacteria 82 0.01%
Hypersaline (saline) Bacteroidetes 114614 12.4%
Hypersaline (saline) Caldiserica 1 0%
Hypersaline (saline) Candidate division OP3 364 0.04%
Hypersaline (saline) Candidate division SR1 34 0%
Hypersaline (saline) Chlamydiae 15 0%
Hypersaline (saline) Chlorobi 462 0.05%
Hypersaline (saline) Chloroflexi 18848 2.04%
Hypersaline (saline) Cloacimonetes 26 0%
Hypersaline (saline) Crenarchaeota 1 0%
Hypersaline (saline) Cyanobacteria 8149 0.88%
Hypersaline (saline) Deferribacteres 394 0.04%
Hypersaline (saline) Deinococcus-Thermus 4400 0.48%
Hypersaline (saline) Elusimicrobia 107 0.01%
Hypersaline (saline) Euryarchaeota 304473 32.95%
Hypersaline (saline) Fibrobacteres 330 0.04%
Hypersaline (saline) Firmicutes 6631 0.72%
Hypersaline (saline) Fusobacteria 77 0.01%
Hypersaline (saline) GAL08 1 0%
Hypersaline (saline) Gemmatimonadetes 4860 0.53%
Hypersaline (saline) Gracilibacteria 119 0.01%
Hypersaline (saline) Hyd24-12 508 0.05%
Hypersaline (saline) Hydrogenedentes 165 0.02%
Hypersaline (saline) JL-ETNP-Z39 27 0%
Hypersaline (saline) Kazan-3B-09 5 0%
Hypersaline (saline) Latescibacteria 1358 0.15%
Hypersaline (saline) LCP-89 80 0.01%
Hypersaline (saline) LD1-PA38 6 0%
Hypersaline (saline) Lentisphaerae 3160 0.34%
Hypersaline (saline) Marinimicrobia (SAR406 clade) 1611 0.17%
Hypersaline (saline) Microgenomates 29 0%
Hypersaline (saline) Miscellaneous Crenarchaeotic Group 279 0.03%
Hypersaline (saline) Nanohaloarchaeota 1761 0.19%
Hypersaline (saline) Nitrospirae 1651 0.18%
Hypersaline (saline) Omnitrophica 306 0.03%
Hypersaline (saline) Parcubacteria 400 0.04%
Hypersaline (saline) PAUC34f 147 0.02%
Hypersaline (saline) Planctomycetes 12674 1.37%
Hypersaline (saline) Proteobacteria 333511 36.09%
Hypersaline (saline) Saccharibacteria 1 0%
Hypersaline (saline) SHA-109 14 0%
Hypersaline (saline) Spirochaetae 5920 0.64%
Hypersaline (saline) TA06 1053 0.11%
Hypersaline (saline) Tenericutes 13494 1.46%
Hypersaline (saline) Thaumarchaeota 5658 0.61%
Hypersaline (saline) Thermotogae 12 0%
Hypersaline (saline) TM6 59 0.01%
Hypersaline (saline) Verrucomicrobia 2701 0.29%
Hypersaline (saline) WD272 2 0%
Hypersaline (saline) Woesearchaeota (DHVEG-6) 920 0.1%
Plant corpus Acetothermia 11 0%
Plant corpus Acidobacteria 11648 0.07%
Plant corpus Actinobacteria 403923 2.53%
Plant corpus Aerophobetes 140 0%
Plant corpus Aminicenantes 218 0%
Plant corpus aquifer1 9 0%
Plant corpus Aquificae 1 0%
Plant corpus Armatimonadetes 1494 0.01%
Plant corpus Atribacteria 291 0%
Plant corpus Bacteroidetes 160603 1.01%
Plant corpus Candidate division OP3 21 0%
Plant corpus Candidate division SR1 15 0%
Plant corpus Chlamydiae 48 0%
Plant corpus Chlorobi 139 0%
Plant corpus Chloroflexi 3944 0.02%
Plant corpus Cyanobacteria 12360725 77.48%
Plant corpus Deferribacteres 34 0%
Plant corpus Deinococcus-Thermus 1869 0.01%
Plant corpus Elusimicrobia 8 0%
Plant corpus Euryarchaeota 293 0%
Plant corpus Fibrobacteres 71 0%
Plant corpus Firmicutes 177325 1.11%
Plant corpus Fusobacteria 12825 0.08%
Plant corpus Gemmatimonadetes 1787 0.01%
Plant corpus Gracilibacteria 15 0%
Plant corpus Hydrogenedentes 122 0%
Plant corpus JL-ETNP-Z39 21 0%
Plant corpus Latescibacteria 14 0%
Plant corpus Lentisphaerae 25 0%
Plant corpus Marinimicrobia (SAR406 clade) 11 0%
Plant corpus Microgenomates 11 0%
Plant corpus Miscellaneous Crenarchaeotic Group 8 0%
Plant corpus Nitrospirae 427 0%
Plant corpus Omnitrophica 40 0%
Plant corpus Parcubacteria 2 0%
Plant corpus Planctomycetes 3647 0.02%
Plant corpus Proteobacteria 2799980 17.55%
Plant corpus Saccharibacteria 246 0%
Plant corpus SHA-109 28 0%
Plant corpus SM2F11 1 0%
Plant corpus Spirochaetae 207 0%
Plant corpus Synergistetes 41 0%
Plant corpus TA06 6 0%
Plant corpus Tenericutes 3237 0.02%
Plant corpus Thaumarchaeota 3763 0.02%
Plant corpus Thermotogae 1 0%
Plant corpus TM6 37 0%
Plant corpus Verrucomicrobia 3973 0.02%
Plant corpus WCHB1-60 34 0%
Plant corpus WD272 1 0%
Plant corpus Woesearchaeota (DHVEG-6) 2 0%
Plant rhizosphere Acidobacteria 1845110 14.46%
Plant rhizosphere Actinobacteria 591199 4.63%
Plant rhizosphere Aenigmarchaeota 369 0%
Plant rhizosphere Aerophobetes 391 0%
Plant rhizosphere Aminicenantes 2904 0.02%
Plant rhizosphere Armatimonadetes 53517 0.42%
Plant rhizosphere Atribacteria 1 0%
Plant rhizosphere Bacteroidetes 1274309 9.99%
Plant rhizosphere Caldiserica 334 0%
Plant rhizosphere Candidate division OP3 7632 0.06%
Plant rhizosphere Candidate division SR1 504 0%
Plant rhizosphere Chlamydiae 4828 0.04%
Plant rhizosphere Chlorobi 146367 1.15%
Plant rhizosphere Chloroflexi 553957 4.34%
Plant rhizosphere CKC4 2 0%
Plant rhizosphere Cloacimonetes 186 0%
Plant rhizosphere Cyanobacteria 422028 3.31%
Plant rhizosphere Deferribacteres 316 0%
Plant rhizosphere Deinococcus-Thermus 4420 0.03%
Plant rhizosphere Diapherotrites 4 0%
Plant rhizosphere Dictyoglomi 2 0%
Plant rhizosphere Elusimicrobia 28048 0.22%
Plant rhizosphere Euryarchaeota 105898 0.83%
Plant rhizosphere Fibrobacteres 19751 0.15%
Plant rhizosphere Firmicutes 264820 2.08%
Plant rhizosphere Fusobacteria 615 0%
Plant rhizosphere GAL08 120 0%
Plant rhizosphere Gemmatimonadetes 193921 1.52%
Plant rhizosphere GOUTA4 5137 0.04%
Plant rhizosphere Gracilibacteria 1531 0.01%
Plant rhizosphere Hydrogenedentes 4302 0.03%
Plant rhizosphere JL-ETNP-Z39 432 0%
Plant rhizosphere Kazan-3B-09 48 0%
Plant rhizosphere Latescibacteria 41768 0.33%
Plant rhizosphere Lentisphaerae 4903 0.04%
Plant rhizosphere Marine Hydrothermal Vent Group(MHVG) 17 0%
Plant rhizosphere Marinimicrobia (SAR406 clade) 142 0%
Plant rhizosphere Microgenomates 2187 0.02%
Plant rhizosphere Miscellaneous Crenarchaeotic Group 18573 0.15%
Plant rhizosphere Miscellaneous Euryarchaeotic Group(MEG) 32 0%
Plant rhizosphere Nitrospirae 187989 1.47%
Plant rhizosphere OC31 10 0%
Plant rhizosphere Omnitrophica 6420 0.05%
Plant rhizosphere Parcubacteria 5648 0.04%
Plant rhizosphere Parvarchaeota 829 0.01%
Plant rhizosphere PAUC34f 228 0%
Plant rhizosphere Planctomycetes 313880 2.46%
Plant rhizosphere Proteobacteria 5742756 45.02%
Plant rhizosphere Saccharibacteria 883 0.01%
Plant rhizosphere SHA-109 465 0%
Plant rhizosphere SM1K20 774 0.01%
Plant rhizosphere SM2F11 2753 0.02%
Plant rhizosphere Spirochaetae 64318 0.5%
Plant rhizosphere Synergistetes 26 0%
Plant rhizosphere TA06 4950 0.04%
Plant rhizosphere Tenericutes 265 0%
Plant rhizosphere Thaumarchaeota 75252 0.59%
Plant rhizosphere Thermotogae 306 0%
Plant rhizosphere TM6 3307 0.03%
Plant rhizosphere Verrucomicrobia 733698 5.75%
Plant rhizosphere WCHB1-60 2797 0.02%
Plant rhizosphere WD272 87 0%
Plant rhizosphere Woesearchaeota (DHVEG-6) 8614 0.07%
Plant surface Acidobacteria 72806 0.56%
Plant surface Actinobacteria 588202 4.53%
Plant surface Aerophobetes 29 0%
Plant surface Armatimonadetes 1164 0.01%
Plant surface Atribacteria 1 0%
Plant surface Bacteroidetes 2114039 16.27%
Plant surface Candidate division OP3 34 0%
Plant surface Candidate division SR1 68 0%
Plant surface Chlamydiae 243 0%
Plant surface Chlorobi 664 0.01%
Plant surface Chloroflexi 22062 0.17%
Plant surface Cloacimonetes 1 0%
Plant surface Cyanobacteria 741341 5.71%
Plant surface Deferribacteres 11 0%
Plant surface Deinococcus-Thermus 13449 0.1%
Plant surface Elusimicrobia 736 0.01%
Plant surface Euryarchaeota 336 0%
Plant surface Fibrobacteres 87 0%
Plant surface Firmicutes 48050 0.37%
Plant surface Fusobacteria 4605 0.04%
Plant surface Gemmatimonadetes 16626 0.13%
Plant surface Gracilibacteria 3973 0.03%
Plant surface Hydrogenedentes 16 0%
Plant surface JL-ETNP-Z39 3 0%
Plant surface Latescibacteria 2228 0.02%
Plant surface Lentisphaerae 497 0%
Plant surface Marinimicrobia (SAR406 clade) 81 0%
Plant surface Microgenomates 15 0%
Plant surface Nitrospirae 3109 0.02%
Plant surface Omnitrophica 128 0%
Plant surface Parcubacteria 287 0%
Plant surface PAUC34f 27 0%
Plant surface Planctomycetes 824288 6.34%
Plant surface Proteobacteria 7736640 59.55%
Plant surface Saccharibacteria 32 0%
Plant surface SHA-109 667 0.01%
Plant surface SM2F11 76 0%
Plant surface Spirochaetae 77 0%
Plant surface Synergistetes 1 0%
Plant surface TA06 1 0%
Plant surface Tenericutes 53 0%
Plant surface Thaumarchaeota 4756 0.04%
Plant surface Thermotogae 10 0%
Plant surface TM6 238 0%
Plant surface Verrucomicrobia 789613 6.08%
Plant surface WCHB1-60 107 0%
Plant surface WD272 18 0%
Plant surface Woesearchaeota (DHVEG-6) 11 0%
Sediment (non-saline) Acetothermia 88 0%
Sediment (non-saline) Acidobacteria 756499 9.23%
Sediment (non-saline) Actinobacteria 359605 4.39%
Sediment (non-saline) Aenigmarchaeota 16721 0.2%
Sediment (non-saline) Aerophobetes 307 0%
Sediment (non-saline) Aminicenantes 60421 0.74%
Sediment (non-saline) aquifer1 4 0%
Sediment (non-saline) Aquificae 2 0%
Sediment (non-saline) Armatimonadetes 17176 0.21%
Sediment (non-saline) Atribacteria 6934 0.08%
Sediment (non-saline) Bacteroidetes 582641 7.11%
Sediment (non-saline) Caldiserica 550 0.01%
Sediment (non-saline) Candidate division OP3 39051 0.48%
Sediment (non-saline) Candidate division SR1 621 0.01%
Sediment (non-saline) Chlamydiae 1673 0.02%
Sediment (non-saline) Chlorobi 94785 1.16%
Sediment (non-saline) Chloroflexi 405243 4.94%
Sediment (non-saline) CKC4 84 0%
Sediment (non-saline) Cloacimonetes 202 0%
Sediment (non-saline) Crenarchaeota 6941 0.08%
Sediment (non-saline) Cyanobacteria 181583 2.21%
Sediment (non-saline) Deferribacteres 33172 0.4%
Sediment (non-saline) Deinococcus-Thermus 9001 0.11%
Sediment (non-saline) Diapherotrites 24 0%
Sediment (non-saline) Dictyoglomi 1 0%
Sediment (non-saline) Elusimicrobia 12935 0.16%
Sediment (non-saline) Euryarchaeota 151630 1.85%
Sediment (non-saline) Fibrobacteres 5761 0.07%
Sediment (non-saline) Firmicutes 152958 1.87%
Sediment (non-saline) Fusobacteria 272 0%
Sediment (non-saline) GAL08 191 0%
Sediment (non-saline) Gemmatimonadetes 134999 1.65%
Sediment (non-saline) GOUTA4 2663 0.03%
Sediment (non-saline) Gracilibacteria 1910 0.02%
Sediment (non-saline) Hyd24-12 120 0%
Sediment (non-saline) Hydrogenedentes 4142 0.05%
Sediment (non-saline) JL-ETNP-Z39 677 0.01%
Sediment (non-saline) Kazan-3B-09 850 0.01%
Sediment (non-saline) Latescibacteria 43904 0.54%
Sediment (non-saline) LCP-89 182 0%
Sediment (non-saline) LD1-PA38 9 0%
Sediment (non-saline) Lentisphaerae 11508 0.14%
Sediment (non-saline) Marine Hydrothermal Vent Group(MHVG) 86 0%
Sediment (non-saline) Marinimicrobia (SAR406 clade) 1163 0.01%
Sediment (non-saline) Microgenomates 699 0.01%
Sediment (non-saline) Miscellaneous Crenarchaeotic Group 173745 2.12%
Sediment (non-saline) Miscellaneous Euryarchaeotic Group(MEG) 332 0%
Sediment (non-saline) Nitrospirae 292186 3.56%
Sediment (non-saline) OC31 2465 0.03%
Sediment (non-saline) Omnitrophica 6774 0.08%
Sediment (non-saline) Parcubacteria 4000 0.05%
Sediment (non-saline) Parvarchaeota 100 0%
Sediment (non-saline) PAUC34f 1483 0.02%
Sediment (non-saline) Planctomycetes 216888 2.65%
Sediment (non-saline) Proteobacteria 3919770 47.81%
Sediment (non-saline) Saccharibacteria 194 0%
Sediment (non-saline) SHA-109 802 0.01%
Sediment (non-saline) SM1K20 1308 0.02%
Sediment (non-saline) SM2F11 520 0.01%
Sediment (non-saline) Spirochaetae 25867 0.32%
Sediment (non-saline) Synergistetes 386 0%
Sediment (non-saline) TA06 38984 0.48%
Sediment (non-saline) Tenericutes 837 0.01%
Sediment (non-saline) Thaumarchaeota 71512 0.87%
Sediment (non-saline) Thermotogae 35 0%
Sediment (non-saline) TM6 3220 0.04%
Sediment (non-saline) uncultured archaeon 32 0%
Sediment (non-saline) Verrucomicrobia 321911 3.93%
Sediment (non-saline) WCHB1-60 717 0.01%
Sediment (non-saline) WD272 1612 0.02%
Sediment (non-saline) Woesearchaeota (DHVEG-6) 12906 0.16%
Sediment (saline) Acetothermia 1247 0.01%
Sediment (saline) Acidobacteria 590604 4.29%
Sediment (saline) Actinobacteria 327052 2.38%
Sediment (saline) Aenigmarchaeota 329 0%
Sediment (saline) Aerophobetes 35502 0.26%
Sediment (saline) Aigarchaeota 21 0%
Sediment (saline) Aminicenantes 24317 0.18%
Sediment (saline) Ancient Archaeal Group(AAG) 1347 0.01%
Sediment (saline) aquifer1 2140 0.02%
Sediment (saline) Armatimonadetes 7397 0.05%
Sediment (saline) Atribacteria 983436 7.15%
Sediment (saline) Bacteroidetes 1490460 10.83%
Sediment (saline) Caldiserica 326 0%
Sediment (saline) Candidate division OP3 12604 0.09%
Sediment (saline) Candidate division SR1 1575 0.01%
Sediment (saline) Chlamydiae 2675 0.02%
Sediment (saline) Chlorobi 50015 0.36%
Sediment (saline) Chloroflexi 380903 2.77%
Sediment (saline) Chrysiogenetes 1 0%
Sediment (saline) CKC4 19 0%
Sediment (saline) Cloacimonetes 3226 0.02%
Sediment (saline) Crenarchaeota 1 0%
Sediment (saline) Cyanobacteria 245168 1.78%
Sediment (saline) Deferribacteres 27461 0.2%
Sediment (saline) Deinococcus-Thermus 6808 0.05%
Sediment (saline) Diapherotrites 33 0%
Sediment (saline) Dictyoglomi 4 0%
Sediment (saline) Elusimicrobia 5105 0.04%
Sediment (saline) Euryarchaeota 157748 1.15%
Sediment (saline) Fibrobacteres 7873 0.06%
Sediment (saline) Firmicutes 444452 3.23%
Sediment (saline) Fusobacteria 24249 0.18%
Sediment (saline) GAL08 4 0%
Sediment (saline) Gemmatimonadetes 76145 0.55%
Sediment (saline) GOUTA4 311 0%
Sediment (saline) Gracilibacteria 6211 0.05%
Sediment (saline) Hyd24-12 8991 0.07%
Sediment (saline) Hydrogenedentes 7288 0.05%
Sediment (saline) JL-ETNP-Z39 708 0.01%
Sediment (saline) Kazan-3B-09 1497 0.01%
Sediment (saline) Latescibacteria 51000 0.37%
Sediment (saline) LCP-89 1100 0.01%
Sediment (saline) LD1-PA38 247 0%
Sediment (saline) Lentisphaerae 55618 0.4%
Sediment (saline) Marine Hydrothermal Vent Group(MHVG) 2390 0.02%
Sediment (saline) Marinimicrobia (SAR406 clade) 18059 0.13%
Sediment (saline) Microgenomates 2871 0.02%
Sediment (saline) Miscellaneous Crenarchaeotic Group 6267 0.05%
Sediment (saline) Miscellaneous Euryarchaeotic Group(MEG) 19 0%
Sediment (saline) Nanohaloarchaeota 173 0%
Sediment (saline) Nitrospirae 44673 0.32%
Sediment (saline) OC31 252 0%
Sediment (saline) Omnitrophica 5867 0.04%
Sediment (saline) Parcubacteria 7781 0.06%
Sediment (saline) Parvarchaeota 2 0%
Sediment (saline) PAUC34f 3410 0.02%
Sediment (saline) Planctomycetes 216790 1.58%
Sediment (saline) Proteobacteria 7667735 55.72%
Sediment (saline) RsaHF231 6 0%
Sediment (saline) Saccharibacteria 348 0%
Sediment (saline) SBYG-2791 5 0%
Sediment (saline) SHA-109 1435 0.01%
Sediment (saline) SM1K20 14 0%
Sediment (saline) SM2F11 305 0%
Sediment (saline) Spirochaetae 71715 0.52%
Sediment (saline) Synergistetes 530 0%
Sediment (saline) TA06 16875 0.12%
Sediment (saline) Tenericutes 16848 0.12%
Sediment (saline) Thaumarchaeota 183805 1.34%
Sediment (saline) Thermotogae 223 0%
Sediment (saline) TM6 4990 0.04%
Sediment (saline) uncultured archaeon 1217 0.01%
Sediment (saline) uncultured bacterium 39 0%
Sediment (saline) Verrucomicrobia 410560 2.98%
Sediment (saline) WCHB1-60 527 0%
Sediment (saline) WD272 650 0%
Sediment (saline) Woesearchaeota (DHVEG-6) 32339 0.23%
Soil (non-saline) Acidobacteria 2745324 19.61%
Soil (non-saline) Actinobacteria 1243107 8.88%
Soil (non-saline) Aenigmarchaeota 60 0%
Soil (non-saline) Aerophobetes 562 0%
Soil (non-saline) Aigarchaeota 4043 0.03%
Soil (non-saline) Aminicenantes 965 0.01%
Soil (non-saline) aquifer1 56 0%
Soil (non-saline) Aquificae 15461 0.11%
Soil (non-saline) Armatimonadetes 50162 0.36%
Soil (non-saline) Atribacteria 174 0%
Soil (non-saline) Bacteroidetes 1567432 11.19%
Soil (non-saline) Caldiserica 4530 0.03%
Soil (non-saline) Candidate division OP3 4211 0.03%
Soil (non-saline) Candidate division SR1 440 0%
Soil (non-saline) Chlamydiae 8301 0.06%
Soil (non-saline) Chlorobi 46480 0.33%
Soil (non-saline) Chloroflexi 290621 2.08%
Soil (non-saline) CKC4 2 0%
Soil (non-saline) Cloacimonetes 24 0%
Soil (non-saline) Crenarchaeota 17393 0.12%
Soil (non-saline) Cyanobacteria 108375 0.77%
Soil (non-saline) Deferribacteres 160 0%
Soil (non-saline) Deinococcus-Thermus 6083 0.04%
Soil (non-saline) Diapherotrites 1 0%
Soil (non-saline) Dictyoglomi 1 0%
Soil (non-saline) Elusimicrobia 27753 0.2%
Soil (non-saline) Euryarchaeota 17627 0.13%
Soil (non-saline) Fibrobacteres 7907 0.06%
Soil (non-saline) Firmicutes 713447 5.1%
Soil (non-saline) Fusobacteria 12458 0.09%
Soil (non-saline) GAL08 44 0%
Soil (non-saline) Gemmatimonadetes 298450 2.13%
Soil (non-saline) GOUTA4 477 0%
Soil (non-saline) Gracilibacteria 397 0%
Soil (non-saline) Hyd24-12 1 0%
Soil (non-saline) Hydrogenedentes 2145 0.02%
Soil (non-saline) JL-ETNP-Z39 1827 0.01%
Soil (non-saline) Kazan-3B-09 7 0%
Soil (non-saline) Latescibacteria 31882 0.23%
Soil (non-saline) Lentisphaerae 3993 0.03%
Soil (non-saline) Marine Hydrothermal Vent Group(MHVG) 2 0%
Soil (non-saline) Marinimicrobia (SAR406 clade) 32 0%
Soil (non-saline) Microgenomates 1888 0.01%
Soil (non-saline) Miscellaneous Crenarchaeotic Group 3186 0.02%
Soil (non-saline) Miscellaneous Euryarchaeotic Group(MEG) 17 0%
Soil (non-saline) Nitrospirae 122150 0.87%
Soil (non-saline) OC31 2 0%
Soil (non-saline) Omnitrophica 2620 0.02%
Soil (non-saline) Parcubacteria 3130 0.02%
Soil (non-saline) Parvarchaeota 56 0%
Soil (non-saline) PAUC34f 52 0%
Soil (non-saline) Planctomycetes 251808 1.8%
Soil (non-saline) Proteobacteria 4787424 34.19%
Soil (non-saline) RsaHF231 3 0%
Soil (non-saline) Saccharibacteria 1394 0.01%
Soil (non-saline) SHA-109 1093 0.01%
Soil (non-saline) SM1K20 48 0%
Soil (non-saline) SM2F11 2751 0.02%
Soil (non-saline) Spirochaetae 5463 0.04%
Soil (non-saline) Synergistetes 71 0%
Soil (non-saline) TA06 769 0.01%
Soil (non-saline) Tenericutes 8464 0.06%
Soil (non-saline) Thaumarchaeota 96389 0.69%
Soil (non-saline) Thermotogae 827 0.01%
Soil (non-saline) TM6 5761 0.04%
Soil (non-saline) uncultured archaeon 246 0%
Soil (non-saline) Verrucomicrobia 1442243 10.3%
Soil (non-saline) WCHB1-60 3901 0.03%
Soil (non-saline) WD272 26823 0.19%
Soil (non-saline) Woesearchaeota (DHVEG-6) 1264 0.01%
Surface (non-saline) Acetothermia 1847 0.02%
Surface (non-saline) Acidobacteria 614776 6.57%
Surface (non-saline) Actinobacteria 867881 9.28%
Surface (non-saline) Aerophobetes 329 0%
Surface (non-saline) Aigarchaeota 1262 0.01%
Surface (non-saline) Aminicenantes 255 0%
Surface (non-saline) aquifer1 138 0%
Surface (non-saline) Aquificae 19316 0.21%
Surface (non-saline) Armatimonadetes 49233 0.53%
Surface (non-saline) Atribacteria 312 0%
Surface (non-saline) Bacteroidetes 648248 6.93%
Surface (non-saline) Caldiserica 871 0.01%
Surface (non-saline) Calescamantes 27 0%
Surface (non-saline) Candidate division OP3 2401 0.03%
Surface (non-saline) Candidate division SR1 5389 0.06%
Surface (non-saline) Candidate division WS6 3 0%
Surface (non-saline) Chlamydiae 24467 0.26%
Surface (non-saline) Chlorobi 41754 0.45%
Surface (non-saline) Chloroflexi 175841 1.88%
Surface (non-saline) CKC4 15 0%
Surface (non-saline) Cloacimonetes 8 0%
Surface (non-saline) Crenarchaeota 1 0%
Surface (non-saline) Cyanobacteria 480236 5.14%
Surface (non-saline) Deferribacteres 836 0.01%
Surface (non-saline) Deinococcus-Thermus 39626 0.42%
Surface (non-saline) Diapherotrites 96 0%
Surface (non-saline) Dictyoglomi 1 0%
Surface (non-saline) Elusimicrobia 3787 0.04%
Surface (non-saline) Euryarchaeota 5388 0.06%
Surface (non-saline) Fibrobacteres 607 0.01%
Surface (non-saline) Firmicutes 1145655 12.25%
Surface (non-saline) Fusobacteria 60652 0.65%
Surface (non-saline) GAL08 85 0%
Surface (non-saline) Gemmatimonadetes 69596 0.74%
Surface (non-saline) GOUTA4 119 0%
Surface (non-saline) Gracilibacteria 2848 0.03%
Surface (non-saline) Hyd24-12 49 0%
Surface (non-saline) Hydrogenedentes 2173 0.02%
Surface (non-saline) JL-ETNP-Z39 210 0%
Surface (non-saline) Kazan-3B-09 16 0%
Surface (non-saline) Latescibacteria 21691 0.23%
Surface (non-saline) LCP-89 58 0%
Surface (non-saline) Lentisphaerae 3243 0.03%
Surface (non-saline) Marinimicrobia (SAR406 clade) 123 0%
Surface (non-saline) Microgenomates 1006 0.01%
Surface (non-saline) Miscellaneous Crenarchaeotic Group 26 0%
Surface (non-saline) Miscellaneous Euryarchaeotic Group(MEG) 495 0.01%
Surface (non-saline) Nitrospirae 148422 1.59%
Surface (non-saline) OC31 5 0%
Surface (non-saline) Omnitrophica 1408 0.02%
Surface (non-saline) Parcubacteria 3071 0.03%
Surface (non-saline) Parvarchaeota 9 0%
Surface (non-saline) PAUC34f 213 0%
Surface (non-saline) Planctomycetes 169615 1.81%
Surface (non-saline) Proteobacteria 4195241 44.86%
Surface (non-saline) RsaHF231 1 0%
Surface (non-saline) S2R-29 1657 0.02%
Surface (non-saline) Saccharibacteria 460 0%
Surface (non-saline) SHA-109 494 0.01%
Surface (non-saline) SM1K20 1 0%
Surface (non-saline) SM2F11 1416 0.02%
Surface (non-saline) Spirochaetae 1937 0.02%
Surface (non-saline) Synergistetes 67 0%
Surface (non-saline) TA06 4826 0.05%
Surface (non-saline) Tenericutes 285008 3.05%
Surface (non-saline) Thaumarchaeota 35957 0.38%
Surface (non-saline) Thermodesulfobacteria 4 0%
Surface (non-saline) Thermotogae 11029 0.12%
Surface (non-saline) TM6 6330 0.07%
Surface (non-saline) uncultured archaeon 1 0%
Surface (non-saline) Verrucomicrobia 189643 2.03%
Surface (non-saline) WCHB1-60 421 0%
Surface (non-saline) WD272 152 0%
Surface (non-saline) Woesearchaeota (DHVEG-6) 610 0.01%
Surface (saline) Acetothermia 8257 0.05%
Surface (saline) Acidobacteria 160810 0.9%
Surface (saline) Actinobacteria 586234 3.28%
Surface (saline) Aenigmarchaeota 24 0%
Surface (saline) Aerophobetes 435 0%
Surface (saline) Aminicenantes 1391 0.01%
Surface (saline) Ancient Archaeal Group(AAG) 2 0%
Surface (saline) aquifer1 45 0%
Surface (saline) Aquificae 12605 0.07%
Surface (saline) Armatimonadetes 14484 0.08%
Surface (saline) Atribacteria 3530 0.02%
Surface (saline) Bacteroidetes 2444346 13.66%
Surface (saline) Caldiserica 22 0%
Surface (saline) Candidate division OP3 6423 0.04%
Surface (saline) Candidate division SR1 1490 0.01%
Surface (saline) Chlamydiae 962 0.01%
Surface (saline) Chlorobi 21168 0.12%
Surface (saline) Chloroflexi 95925 0.54%
Surface (saline) CKC4 5 0%
Surface (saline) Cloacimonetes 723 0%
Surface (saline) Cyanobacteria 2678289 14.97%
Surface (saline) Deferribacteres 12332 0.07%
Surface (saline) Deinococcus-Thermus 5101 0.03%
Surface (saline) Diapherotrites 7 0%
Surface (saline) Dictyoglomi 10 0%
Surface (saline) Elusimicrobia 1933 0.01%
Surface (saline) Euryarchaeota 12863 0.07%
Surface (saline) Fibrobacteres 2937 0.02%
Surface (saline) Firmicutes 1200575 6.71%
Surface (saline) Fusobacteria 22255 0.12%
Surface (saline) Gemmatimonadetes 31259 0.17%
Surface (saline) GOUTA4 38 0%
Surface (saline) Gracilibacteria 12179 0.07%
Surface (saline) Hyd24-12 453 0%
Surface (saline) Hydrogenedentes 2088 0.01%
Surface (saline) JL-ETNP-Z39 290 0%
Surface (saline) Kazan-3B-09 107 0%
Surface (saline) Latescibacteria 13076 0.07%
Surface (saline) LCP-89 52 0%
Surface (saline) LD1-PA38 80 0%
Surface (saline) Lentisphaerae 29810 0.17%
Surface (saline) Marine Hydrothermal Vent Group(MHVG) 33 0%
Surface (saline) Marinimicrobia (SAR406 clade) 5087 0.03%
Surface (saline) Microgenomates 288 0%
Surface (saline) Miscellaneous Crenarchaeotic Group 429 0%
Surface (saline) Miscellaneous Euryarchaeotic Group(MEG) 3 0%
Surface (saline) Nitrospirae 154614 0.86%
Surface (saline) OC31 19 0%
Surface (saline) Omnitrophica 32428 0.18%
Surface (saline) Parcubacteria 7031 0.04%
Surface (saline) Parvarchaeota 7 0%
Surface (saline) PAUC34f 1307 0.01%
Surface (saline) Planctomycetes 389389 2.18%
Surface (saline) Proteobacteria 9387089 52.47%
Surface (saline) RsaHF231 2 0%
Surface (saline) Saccharibacteria 191 0%
Surface (saline) SHA-109 1912 0.01%
Surface (saline) SM1K20 7 0%
Surface (saline) SM2F11 436 0%
Surface (saline) Spirochaetae 11773 0.07%
Surface (saline) Synergistetes 311 0%
Surface (saline) TA06 890 0%
Surface (saline) Tenericutes 3870 0.02%
Surface (saline) Thaumarchaeota 34129 0.19%
Surface (saline) Thermotogae 118 0%
Surface (saline) TM6 2907 0.02%
Surface (saline) uncultured archaeon 225 0%
Surface (saline) Verrucomicrobia 464163 2.59%
Surface (saline) WCHB1-60 1621 0.01%
Surface (saline) WD272 22 0%
Surface (saline) Woesearchaeota (DHVEG-6) 6211 0.03%
Water (non-saline) Acetothermia 198 0%
Water (non-saline) Acidobacteria 366560 1.81%
Water (non-saline) Actinobacteria 3250148 16.05%
Water (non-saline) Aenigmarchaeota 147 0%
Water (non-saline) Aerophobetes 192 0%
Water (non-saline) Aminicenantes 18375 0.09%
Water (non-saline) aquifer1 89 0%
Water (non-saline) Armatimonadetes 33499 0.17%
Water (non-saline) Atribacteria 660 0%
Water (non-saline) Bacteroidetes 3422394 16.9%
Water (non-saline) Caldiserica 145 0%
Water (non-saline) Candidate division OP3 22010 0.11%
Water (non-saline) Candidate division SR1 2431 0.01%
Water (non-saline) Chlamydiae 8676 0.04%
Water (non-saline) Chlorobi 112650 0.56%
Water (non-saline) Chloroflexi 350766 1.73%
Water (non-saline) CKC4 221 0%
Water (non-saline) Cloacimonetes 1465 0.01%
Water (non-saline) Crenarchaeota 258 0%
Water (non-saline) Cyanobacteria 2945876 14.55%
Water (non-saline) Deferribacteres 1791 0.01%
Water (non-saline) Deinococcus-Thermus 2509 0.01%
Water (non-saline) Diapherotrites 68 0%
Water (non-saline) Dictyoglomi 7 0%
Water (non-saline) Elusimicrobia 13723 0.07%
Water (non-saline) Euryarchaeota 28563 0.14%
Water (non-saline) Fibrobacteres 4194 0.02%
Water (non-saline) Firmicutes 467255 2.31%
Water (non-saline) Fusobacteria 15785 0.08%
Water (non-saline) GAL08 65 0%
Water (non-saline) Gemmatimonadetes 56677 0.28%
Water (non-saline) GOUTA4 586 0%
Water (non-saline) Gracilibacteria 4122 0.02%
Water (non-saline) Hyd24-12 258 0%
Water (non-saline) Hydrogenedentes 1072 0.01%
Water (non-saline) JL-ETNP-Z39 28 0%
Water (non-saline) Kazan-3B-09 283 0%
Water (non-saline) Latescibacteria 11411 0.06%
Water (non-saline) LCP-89 218 0%
Water (non-saline) Lentisphaerae 12794 0.06%
Water (non-saline) Marine Hydrothermal Vent Group(MHVG) 6 0%
Water (non-saline) Marinimicrobia (SAR406 clade) 3385 0.02%
Water (non-saline) Microgenomates 2700 0.01%
Water (non-saline) Miscellaneous Crenarchaeotic Group 16909 0.08%
Water (non-saline) Miscellaneous Euryarchaeotic Group(MEG) 92 0%
Water (non-saline) Nitrospirae 41006 0.2%
Water (non-saline) OC31 78 0%
Water (non-saline) Omnitrophica 12577 0.06%
Water (non-saline) Parcubacteria 28041 0.14%
Water (non-saline) Parvarchaeota 362 0%
Water (non-saline) PAUC34f 438 0%
Water (non-saline) Planctomycetes 360535 1.78%
Water (non-saline) Proteobacteria 7777792 38.41%
Water (non-saline) RsaHF231 30 0%
Water (non-saline) Saccharibacteria 3273 0.02%
Water (non-saline) SHA-109 631 0%
Water (non-saline) SM1K20 716 0%
Water (non-saline) SM2F11 5414 0.03%
Water (non-saline) Spirochaetae 16512 0.08%
Water (non-saline) Synergistetes 211 0%
Water (non-saline) TA06 1999 0.01%
Water (non-saline) Tenericutes 1191 0.01%
Water (non-saline) Thaumarchaeota 16940 0.08%
Water (non-saline) Thermotogae 84 0%
Water (non-saline) TM6 6917 0.03%
Water (non-saline) uncultured archaeon 12 0%
Water (non-saline) Verrucomicrobia 779446 3.85%
Water (non-saline) WCHB1-60 6159 0.03%
Water (non-saline) WD272 188 0%
Water (non-saline) Woesearchaeota (DHVEG-6) 4952 0.02%
Water (saline) Acetothermia 263 0%
Water (saline) Acidobacteria 468181 2.9%
Water (saline) Actinobacteria 542563 3.36%
Water (saline) Aenigmarchaeota 19 0%
Water (saline) Aerophobetes 155 0%
Water (saline) Aigarchaeota 4 0%
Water (saline) Aminicenantes 1776 0.01%
Water (saline) Ancient Archaeal Group(AAG) 2 0%
Water (saline) aquifer1 1 0%
Water (saline) Aquificae 4 0%
Water (saline) Armatimonadetes 1265 0.01%
Water (saline) Atribacteria 706 0%
Water (saline) Bacteroidetes 3730714 23.09%
Water (saline) Caldiserica 227 0%
Water (saline) Candidate division OP3 6202 0.04%
Water (saline) Candidate division SR1 118 0%
Water (saline) Chlamydiae 1017 0.01%
Water (saline) Chlorobi 20001 0.12%
Water (saline) Chloroflexi 133382 0.83%
Water (saline) CKC4 12 0%
Water (saline) Cloacimonetes 8368 0.05%
Water (saline) Crenarchaeota 57 0%
Water (saline) Cyanobacteria 2059139 12.74%
Water (saline) Deferribacteres 4514 0.03%
Water (saline) Deinococcus-Thermus 774 0%
Water (saline) Diapherotrites 15 0%
Water (saline) Dictyoglomi 11 0%
Water (saline) Elusimicrobia 836 0.01%
Water (saline) Euryarchaeota 115673 0.72%
Water (saline) Fibrobacteres 1228 0.01%
Water (saline) Firmicutes 63649 0.39%
Water (saline) Fusobacteria 33730 0.21%
Water (saline) GAL08 10 0%
Water (saline) Gemmatimonadetes 14309 0.09%
Water (saline) GOUTA4 106 0%
Water (saline) Gracilibacteria 2284 0.01%
Water (saline) Hyd24-12 1725 0.01%
Water (saline) Hydrogenedentes 588 0%
Water (saline) JL-ETNP-Z39 155 0%
Water (saline) Kazan-3B-09 384 0%
Water (saline) Latescibacteria 5747 0.04%
Water (saline) LCP-89 518 0%
Water (saline) LD1-PA38 2 0%
Water (saline) Lentisphaerae 6995 0.04%
Water (saline) Marine Hydrothermal Vent Group(MHVG) 23 0%
Water (saline) Marinimicrobia (SAR406 clade) 329714 2.04%
Water (saline) Microgenomates 180 0%
Water (saline) Miscellaneous Crenarchaeotic Group 1505 0.01%
Water (saline) Miscellaneous Euryarchaeotic Group(MEG) 3 0%
Water (saline) Nitrospirae 10304 0.06%
Water (saline) OC31 23 0%
Water (saline) Omnitrophica 921 0.01%
Water (saline) Parcubacteria 1125 0.01%
Water (saline) Parvarchaeota 26 0%
Water (saline) PAUC34f 4057 0.03%
Water (saline) Planctomycetes 105276 0.65%
Water (saline) Proteobacteria 7981764 49.4%
Water (saline) RsaHF231 3 0%
Water (saline) Saccharibacteria 766 0%
Water (saline) SBYG-2791 16 0%
Water (saline) SHA-109 331 0%
Water (saline) SM1K20 45 0%
Water (saline) SM2F11 79 0%
Water (saline) Spirochaetae 15085 0.09%
Water (saline) Synergistetes 76 0%
Water (saline) TA06 2482 0.02%
Water (saline) Tenericutes 2469 0.02%
Water (saline) Thaumarchaeota 93841 0.58%
Water (saline) Thermotogae 49 0%
Water (saline) TM6 1515 0.01%
Water (saline) uncultured archaeon 19 0%
Water (saline) Verrucomicrobia 376298 2.33%
Water (saline) WCHB1-60 41 0%
Water (saline) WD272 256 0%
Water (saline) Woesearchaeota (DHVEG-6) 1609 0.01%
# save summary table
taxa_sum_df %>% 
  filter(Abundance != 0) %>% 
  write.csv(file = paste0("EMP_", Grouping_var,"_", Rank,".csv"))

Plot a heatmap

# Agglomerate taxa
EMP_merge %>% 
  tax_glom(Rank, NArm = TRUE) %>% 
  transform_sample_counts(function(x) x / sum(x) * 100) ->
  Ps_obj_filt_glom

plot_heatmap(
  Ps_obj_filt_glom,
  # method = "NMDS",
  # distance = "bray",
  trans = log_trans(4),
  sample.order = Grouping_var,
  sample.label = Grouping_var,
  taxa.label = Rank,
  taxa.order = Rank_order$OTU
) + 
  theme_bw(base_size = 18) + 
  theme(axis.text.x = element_text(angle = 45.0, vjust = 1, hjust = 1)) +
  scale_fill_viridis(trans = "log", labels = scales::number_format(accuracy = 0.1), option = "magma", na.value = "black") +
  labs(fill = "Abundance (%)")

Plot a bar chart

EMP_merge %>% 
  tax_glom(., Rank) %>% 
  transform_sample_counts(., function(x) x / sum(x) * 100) %>% 
  psmelt() %>%  
  mutate_if(is.character, as.factor) %>% 
  mutate(Phylum = fct_relevel(pull(., Rank), rev(unique(pull(Rank_order, Rank))))) %>% 
  ggplot(aes(fill = !!sym(Rank), x = !!sym(Grouping_var), y = log10(Abundance))) +
  geom_col() +
  theme_set(theme_bw()) +
  theme(axis.text.x = element_text(angle = 45.0, vjust = 1, hjust = 1),
        legend.position = "bottom") +
  labs(y = "Log10 rel. abundance") +
  facet_wrap(~get(Rank), ncol = 5) 

Plot a violin and dot chart

EMP %>% 
  tax_glom(., Rank) %>% 
  transform_sample_counts(., function(x) x / sum(x) * 100) %>% 
  psmelt() %>%  
  mutate_if(is.character, as.factor) %>% 
  mutate(Taxa = fct_relevel(pull(., Rank), rev(unique(pull(Rank_order, Rank))))) %>%
  mutate(Taxa = fct_other(Taxa, drop = pull(Rank_order, Rank)[Rank_order$Abundance < 0.1], other_level = "Rare")) %>% 
  ggplot(aes(x = Taxa, y = Abundance)) +
  geom_violin(aes(group = interaction(Taxa, !!sym(Grouping_var))),
              scale = "width") +
  geom_point2(aes(colour = Taxa), 
              position = position_jitter(width = 0.2),
             alpha = 1/4,
             stroke = 0, 
             size = 2) +
  theme(axis.text = element_text(angle = 45.0), 
        axis.text.x = element_text(vjust = 1, hjust = 1) ) + 
  # scale_fill_locuszoom() +
  # scale_color_manual(values = pal("d3js")[c(3, 4, 2)]) +
  labs(x = NULL, y = "Abundance (%)", colour = Rank) + 
  guides(colour = guide_legend(override.aes = list(size = 5, alpha = 1))) + 
  facet_wrap(~get(Grouping_var), ncol = 2) 

Generate heat-tree plots using Metacoder (Foster, Sharpton, and Grünwald 2017)

# Convert phyloseq to taxmap
EMP %>% 
  # transform_sample_counts(function(x) x / sum(x) ) %>% # not really needed
  parse_phyloseq() %>% 
  taxa::filter_taxa(., !taxon_ranks %in% c("Species", "Genus", "Family", "Order")) -> # tips will be Class
  EMP_taxmap

# Potentially drop out low reads
# EMP_taxmap$data$otu_table <- zero_low_counts(EMP_taxmap, "otu_table", min_count = 5)
# no_reads <- rowSums(EMP_taxmap$data$otu_table[, EMP_taxmap$data$sample_data$sample_id]) == 0
# EMP_taxmap <- filter_obs(EMP_taxmap, data = "tax_data", ! no_reads, drop_taxa = TRUE)

# Sum counts per group
EMP_taxmap$data$tax_counts <- calc_taxon_abund(EMP_taxmap, 
                                                      data = 'otu_table', 
                                                      cols = EMP_taxmap$data$sample_data$sample_id, 
                                                      groups = pull(EMP_taxmap$data$sample_data, Grouping_var))

# Generate a plot for each group
my_plots <- lapply(sort(unique(get_variable(EMP, Grouping_var))), function(group) {
  # do something with time point data
  set.seed(2020) # Make each plot layout look the same if using another layout
  EMP_taxmap %>% 
    heat_tree(.,
              node_label = taxon_names,
              node_size = n_obs,
              node_color = EMP_taxmap$data$tax_counts[[group]],
              node_size_axis_label = 'OTU count',
              node_color_axis_label = 'Sequence count',
              layout = "automatic",
              node_size_range = c(0.013, 0.04), # makes scale range the same in both
              title = group)
})

wrap_plots(my_plots, ncol = 3)

Colophon

sessioninfo::session_info() %>%
  details::details(
    summary = 'Current session info',
    open    = TRUE
  )

Current session info


─ Session info ─────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.0.2 (2020-06-22)
 os       Ubuntu 18.04.5 LTS          
 system   x86_64, linux-gnu           
 ui       X11                         
 language en_GB                       
 collate  en_DK.UTF-8                 
 ctype    en_DK.UTF-8                 
 tz       Europe/Prague               
 date     2020-12-17                  

─ Packages ─────────────────────────────────────────────────────────────────────────────
 package      * version    date       lib source                           
 abind          1.4-5      2016-07-21 [1] CRAN (R 4.0.2)                   
 ade4           1.7-16     2020-10-28 [1] CRAN (R 4.0.2)                   
 ape            5.4-1      2020-08-13 [1] CRAN (R 4.0.2)                   
 assertthat     0.2.1      2019-03-21 [1] CRAN (R 4.0.2)                   
 backports      1.2.1      2020-12-09 [1] CRAN (R 4.0.2)                   
 bayestestR     0.8.0      2020-12-05 [1] CRAN (R 4.0.2)                   
 Biobase        2.48.0     2020-04-27 [1] Bioconductor                     
 BiocGenerics   0.34.0     2020-04-27 [1] Bioconductor                     
 biomformat     1.16.0     2020-04-27 [1] Bioconductor                     
 Biostrings     2.56.0     2020-04-27 [1] Bioconductor                     
 broom          0.7.3      2020-12-16 [1] CRAN (R 4.0.2)                   
 car            3.0-10     2020-09-29 [1] CRAN (R 4.0.2)                   
 carData        3.0-4      2020-05-22 [1] CRAN (R 4.0.2)                   
 cellranger     1.1.0      2016-07-27 [1] CRAN (R 4.0.2)                   
 cli            2.2.0      2020-11-20 [1] CRAN (R 4.0.2)                   
 clipr          0.7.1      2020-10-08 [1] CRAN (R 4.0.2)                   
 cluster        2.1.0      2019-06-19 [1] CRAN (R 4.0.2)                   
 codetools      0.2-18     2020-11-04 [1] CRAN (R 4.0.2)                   
 colorspace     2.0-0      2020-11-11 [1] CRAN (R 4.0.2)                   
 crayon         1.3.4      2017-09-16 [1] CRAN (R 4.0.2)                   
 curl           4.3        2019-12-02 [1] CRAN (R 4.0.2)                   
 data.table     1.13.4     2020-12-08 [1] CRAN (R 4.0.2)                   
 DBI            1.1.0      2019-12-15 [1] CRAN (R 4.0.2)                   
 dbplyr         2.0.0      2020-11-03 [1] CRAN (R 4.0.2)                   
 desc           1.2.0      2018-05-01 [1] CRAN (R 4.0.2)                   
 details        0.2.1      2020-01-12 [1] CRAN (R 4.0.2)                   
 digest         0.6.27     2020-10-24 [1] CRAN (R 4.0.2)                   
 diptest        0.75-7     2016-12-05 [1] CRAN (R 4.0.2)                   
 dplyr        * 1.0.2      2020-08-18 [1] CRAN (R 4.0.2)                   
 effectsize     0.4.1      2020-12-07 [1] CRAN (R 4.0.2)                   
 ellipsis       0.3.1      2020-05-15 [1] CRAN (R 4.0.2)                   
 evaluate       0.14       2019-05-28 [1] CRAN (R 4.0.2)                   
 extrafont    * 0.17       2014-12-08 [1] CRAN (R 4.0.2)                   
 extrafontdb    1.0        2012-06-11 [1] CRAN (R 4.0.2)                   
 fansi          0.4.1      2020-01-08 [1] CRAN (R 4.0.2)                   
 farver         2.0.3      2020-01-16 [1] CRAN (R 4.0.2)                   
 forcats      * 0.5.0      2020-03-01 [1] CRAN (R 4.0.2)                   
 foreach        1.5.1      2020-10-15 [1] CRAN (R 4.0.2)                   
 foreign        0.8-79     2020-04-26 [4] CRAN (R 4.0.0)                   
 fs             1.5.0      2020-07-31 [1] CRAN (R 4.0.2)                   
 gdtools        0.2.2      2020-04-03 [1] CRAN (R 4.0.2)                   
 generics       0.1.0      2020-10-31 [1] CRAN (R 4.0.2)                   
 ggfittext      0.9.0      2020-06-14 [1] CRAN (R 4.0.2)                   
 ggplot2      * 3.3.2      2020-06-19 [1] CRAN (R 4.0.2)                   
 ggpubr         0.4.0      2020-06-27 [1] CRAN (R 4.0.2)                   
 ggrepel        0.9.0      2020-12-16 [1] CRAN (R 4.0.2)                   
 ggridges       0.5.2      2020-01-12 [1] CRAN (R 4.0.2)                   
 ggsignif       0.6.0      2019-08-08 [1] CRAN (R 4.0.2)                   
 ggtext       * 0.1.1      2020-12-17 [1] CRAN (R 4.0.2)                   
 ggthemes       4.2.0      2019-05-13 [1] CRAN (R 4.0.2)                   
 glue           1.4.2      2020-08-27 [1] CRAN (R 4.0.2)                   
 gridExtra      2.3        2017-09-09 [1] CRAN (R 4.0.2)                   
 gridtext       0.1.4      2020-12-10 [1] CRAN (R 4.0.2)                   
 gtable         0.3.0      2019-03-25 [1] CRAN (R 4.0.2)                   
 haven          2.3.1      2020-06-01 [1] CRAN (R 4.0.2)                   
 highr          0.8        2019-03-20 [1] CRAN (R 4.0.2)                   
 hms            0.5.3      2020-01-08 [1] CRAN (R 4.0.2)                   
 htmltools      0.5.0      2020-06-16 [1] CRAN (R 4.0.2)                   
 httr           1.4.2      2020-07-20 [1] CRAN (R 4.0.2)                   
 igraph         1.2.6      2020-10-06 [1] CRAN (R 4.0.2)                   
 insight        0.11.1     2020-12-08 [1] CRAN (R 4.0.2)                   
 IRanges        2.22.2     2020-05-21 [1] Bioconductor                     
 iterators      1.0.13     2020-10-15 [1] CRAN (R 4.0.2)                   
 jsonlite       1.7.2      2020-12-09 [1] CRAN (R 4.0.2)                   
 kableExtra   * 1.3.1      2020-10-22 [1] CRAN (R 4.0.2)                   
 knitr          1.30       2020-09-22 [1] CRAN (R 4.0.2)                   
 labeling       0.4.2      2020-10-20 [1] CRAN (R 4.0.2)                   
 lattice        0.20-41    2020-04-02 [1] CRAN (R 4.0.2)                   
 lazyeval       0.2.2      2019-03-15 [1] CRAN (R 4.0.2)                   
 lifecycle      0.2.0      2020-03-06 [1] CRAN (R 4.0.2)                   
 lubridate      1.7.9.2    2020-11-13 [1] CRAN (R 4.0.2)                   
 magrittr       2.0.1      2020-11-17 [1] CRAN (R 4.0.2)                   
 MASS           7.3-53     2020-09-09 [1] CRAN (R 4.0.2)                   
 Matrix         1.2-18     2019-11-27 [1] CRAN (R 4.0.2)                   
 metacoder    * 0.3.4      2020-04-29 [1] CRAN (R 4.0.2)                   
 mgcv           1.8-33     2020-08-27 [1] CRAN (R 4.0.2)                   
 microbiome     1.10.0     2020-04-27 [1] Bioconductor                     
 MicrobiomeR  * 0.7.0      2020-12-04 [1] Bioconductor                     
 modelr         0.1.8      2020-05-19 [1] CRAN (R 4.0.2)                   
 multtest       2.44.0     2020-04-27 [1] Bioconductor                     
 munsell        0.5.0      2018-06-12 [1] CRAN (R 4.0.2)                   
 nlme           3.1-151    2020-12-10 [1] CRAN (R 4.0.2)                   
 openxlsx       4.2.3      2020-10-27 [1] CRAN (R 4.0.2)                   
 parameters     0.10.1     2020-12-08 [1] CRAN (R 4.0.2)                   
 patchwork    * 1.1.1      2020-12-17 [1] CRAN (R 4.0.2)                   
 permute        0.9-5      2019-03-12 [1] CRAN (R 4.0.2)                   
 phyloseq     * 1.32.0     2020-04-27 [1] Bioconductor                     
 pillar         1.4.7      2020-11-20 [1] CRAN (R 4.0.2)                   
 pkgconfig      2.0.3      2019-09-22 [1] CRAN (R 4.0.2)                   
 plyr           1.8.6      2020-03-03 [1] CRAN (R 4.0.2)                   
 png            0.1-7      2013-12-03 [1] CRAN (R 4.0.2)                   
 prettyunits    1.1.1      2020-01-24 [1] CRAN (R 4.0.2)                   
 progress       1.2.2      2019-05-16 [1] CRAN (R 4.0.2)                   
 ps             1.5.0      2020-12-05 [1] CRAN (R 4.0.2)                   
 purrr        * 0.3.4      2020-04-17 [1] CRAN (R 4.0.2)                   
 R6             2.5.0      2020-10-28 [1] CRAN (R 4.0.2)                   
 Rcpp           1.0.5      2020-07-06 [1] CRAN (R 4.0.2)                   
 readr        * 1.4.0      2020-10-05 [1] CRAN (R 4.0.2)                   
 readxl         1.3.1      2019-03-13 [1] CRAN (R 4.0.2)                   
 reprex         0.3.0      2019-05-16 [1] CRAN (R 4.0.2)                   
 reshape2       1.4.4      2020-04-09 [1] CRAN (R 4.0.2)                   
 rhdf5          2.32.4     2020-10-05 [1] Bioconductor                     
 Rhdf5lib       1.10.1     2020-07-09 [1] Bioconductor                     
 rio            0.5.16     2018-11-26 [1] CRAN (R 4.0.2)                   
 rlang          0.4.9      2020-11-26 [1] CRAN (R 4.0.2)                   
 rmarkdown    * 2.6        2020-12-14 [1] CRAN (R 4.0.2)                   
 rprojroot      2.0.2      2020-11-15 [1] CRAN (R 4.0.2)                   
 rstatix        0.6.0      2020-06-18 [1] CRAN (R 4.0.2)                   
 rstudioapi     0.13       2020-11-12 [1] CRAN (R 4.0.2)                   
 Rtsne          0.15       2018-11-10 [1] CRAN (R 4.0.2)                   
 Rttf2pt1       1.3.8      2020-01-10 [1] CRAN (R 4.0.2)                   
 rvest          0.3.6      2020-07-25 [1] CRAN (R 4.0.2)                   
 S4Vectors      0.26.1     2020-05-16 [1] Bioconductor                     
 scales       * 1.1.1      2020-05-11 [1] CRAN (R 4.0.2)                   
 scico          1.2.0      2020-06-08 [1] CRAN (R 4.0.2)                   
 see          * 0.6.1      2020-12-06 [1] CRAN (R 4.0.2)                   
 sessioninfo    1.1.1      2018-11-05 [1] CRAN (R 4.0.2)                   
 shades         1.4.0      2019-08-02 [1] CRAN (R 4.0.2)                   
 speedyseq    * 0.5.3.9001 2020-10-27 [1] Github (mikemc/speedyseq@8daed32)
 stringi        1.5.3      2020-09-09 [1] CRAN (R 4.0.2)                   
 stringr      * 1.4.0      2019-02-10 [1] CRAN (R 4.0.2)                   
 survival       3.2-7      2020-09-28 [1] CRAN (R 4.0.2)                   
 svglite      * 1.2.3.2    2020-07-07 [1] CRAN (R 4.0.2)                   
 systemfonts    0.3.2      2020-09-29 [1] CRAN (R 4.0.2)                   
 taxa         * 0.3.4.9001 2020-12-04 [1] Github (ropensci/taxa@b3055e9)   
 tibble       * 3.0.4      2020-10-12 [1] CRAN (R 4.0.2)                   
 tidyr        * 1.1.2      2020-08-27 [1] CRAN (R 4.0.2)                   
 tidyselect     1.1.0      2020-05-11 [1] CRAN (R 4.0.2)                   
 tidyverse    * 1.3.0      2019-11-21 [1] CRAN (R 4.0.2)                   
 vctrs          0.3.6      2020-12-17 [1] CRAN (R 4.0.2)                   
 vegan          2.5-7      2020-11-28 [1] CRAN (R 4.0.2)                   
 viridis      * 0.5.1      2018-03-29 [1] CRAN (R 4.0.2)                   
 viridisLite  * 0.3.0      2018-02-01 [1] CRAN (R 4.0.2)                   
 webshot        0.5.2      2019-11-22 [1] CRAN (R 4.0.2)                   
 withr          2.3.0      2020-09-22 [1] CRAN (R 4.0.2)                   
 xfun           0.19       2020-10-30 [1] CRAN (R 4.0.2)                   
 xml2           1.3.2      2020-04-23 [1] CRAN (R 4.0.2)                   
 XVector        0.28.0     2020-04-27 [1] Bioconductor                     
 yaml           2.2.1      2020-02-01 [1] CRAN (R 4.0.2)                   
 zip            2.1.1      2020-08-27 [1] CRAN (R 4.0.2)                   
 zlibbioc       1.34.0     2020-04-27 [1] Bioconductor                     

[1] /home/angel/R/library
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library


References

Foster, Zachary S. L., Thomas J. Sharpton, and Niklaus J. Grünwald. 2017. “Metacoder: An R Package for Visualization and Manipulation of Community Taxonomic Diversity Data.” PLOS Computational Biology 13 (2): e1005404. doi:10.1371/journal.pcbi.1005404.

Thompson, Luke R., Jon G. Sanders, Daniel McDonald, Amnon Amir, Joshua Ladau, Kenneth J. Locey, Robert J. Prill, et al. 2017. “A Communal Catalogue Reveals Earth’s Multiscale Microbial Diversity.” Nature 551 (7681): 457–63. doi:10.1038/nature24621.